With the growing popularity of single-cell RNA-Seq analysis, the t-SNE projection of multi-dimensional data is appearing more often in publications and online. If you’ve ever wanted to develop a better intuitive feel for what exactly t-SNE does and where it can go wrong, this interactive tutorial (by Martin Wattenberg and Fernanda Viegas) is extremely compelling and useful.
In addition to providing a wonderful, interactive plotting function, the authors go on to provide an informative tutorial explains the pitfalls and challenges of the optimization and hyper-parameter tuning of t-SNE projections and how to get the most from the plots. Here is an example:
In the example above, tuning the “perplexity” of the t-SNE projection causes the correct reconstruction of the data when values are between 30-50, but the same method fails when the parameter falls outside those ranges (i.e., too small or too large).
Go check out this distill.pub site. It’s worth your time.